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LIG3 DNA ligase 3 [ Homo sapiens (human) ]

Gene ID: 3980, updated on 15-Aug-2018

Summary

Official Symbol
LIG3provided by HGNC
Official Full Name
DNA ligase 3provided by HGNC
Primary source
HGNC:HGNC:6600
See related
Ensembl:ENSG00000005156 MIM:600940; Vega:OTTHUMG00000128519
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LIG2; LIG3alpha
Summary
This gene is a member of the DNA ligase family. Each member of this family encodes a protein that catalyzes the joining of DNA ends but they each have a distinct role in DNA metabolism. The protein encoded by this gene is involved in excision repair and is located in both the mitochondria and nucleus, with translation initiation from the upstream start codon allowing for transport to the mitochondria and translation initiation from a downstream start codon allowing for transport to the nucleus. Additionally, alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 7.0), thyroid (RPKM 4.6) and 25 other tissues See more
Orthologs

Genomic context

See LIG3 in Genome Data Viewer
Location:
17q12
Exon count:
22
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (34980498..35005828)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (33307517..33332088)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371742 Neighboring gene uncharacterized LOC105371741 Neighboring gene chaperonin containing TCP1 subunit 6B Neighboring gene zinc finger protein 830 Neighboring gene RAD51L3-RFFL readthrough Neighboring gene oligosaccharyltransferase complex subunit pseudogene 7 Neighboring gene ring finger and FYVE like domain containing E3 ubiquitin protein ligase Neighboring gene ribosomal protein L37 pseudogene 22 Neighboring gene RAD51 paralog D

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Common variants at ten loci influence QT interval duration in the QTGEN Study.
NHGRI GWA Catalog
Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, ligase III, DNA, ATP-dependent (LIG3), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with LIG3 is increased by RRE PubMed
Tat tat Both HIV-1 Tat 47-59 and FITC-labeled Tat 47-59 peptides downregulate gene expression of ligase III, DNA, ATP-dependent (LIG3) in U-937 macrophages PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway, organism-specific biosystem (from REACTOME)
    APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway, organism-specific biosystemNEIL1 and NEIL2 have a dual DNA glycosylase and beta/delta lyase activity. The AP (apurinic/apyrimidinic) site-directed lyase activity of NEIL1 and NEIL2 is their major physiological role, as they ca...
  • BER complex, organism-specific biosystem (from KEGG)
    BER complex, organism-specific biosystemStructural complex; Genetic information processing; Repair system
  • BER complex, conserved biosystem (from KEGG)
    BER complex, conserved biosystemStructural complex; Genetic information processing; Repair system
  • Base Excision Repair, organism-specific biosystem (from REACTOME)
    Base Excision Repair, organism-specific biosystemOf the three major pathways involved in the repair of nucleotide damage in DNA, base excision repair (BER) involves the greatest number of individual enzymatic activities. This is the consequence of ...
  • Base excision repair, organism-specific biosystem (from KEGG)
    Base excision repair, organism-specific biosystemBase excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair ...
  • Base excision repair, conserved biosystem (from KEGG)
    Base excision repair, conserved biosystemBase excision repair (BER) is the predominant DNA damage repair pathway for the processing of small base lesions, derived from oxidation and alkylation damages. BER is normally defined as DNA repair ...
  • DNA Double-Strand Break Repair, organism-specific biosystem (from REACTOME)
    DNA Double-Strand Break Repair, organism-specific biosystemNumerous types of DNA damage can occur within a cell due to the endogenous production of oxygen free radicals, normal alkylation reactions, or exposure to exogenous radiations and chemicals. Double-s...
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • Gap-filling DNA repair synthesis and ligation in GG-NER, organism-specific biosystem (from REACTOME)
    Gap-filling DNA repair synthesis and ligation in GG-NER, organism-specific biosystemGlobal genome nucleotide excision repair (GG-NER) is completed by DNA repair synthesis that fills the single stranded gap created after dual incision of the damaged DNA strand and excision of the ~27...
  • Gap-filling DNA repair synthesis and ligation in TC-NER, organism-specific biosystem (from REACTOME)
    Gap-filling DNA repair synthesis and ligation in TC-NER, organism-specific biosystemIn transcription-coupled nucleotide excision repair (TC-NER), similar to global genome nucleotide excision repair (GG-NER), DNA polymerases delta or epsilon, or the Y family DNA polymerase kappa, fil...
  • Global Genome Nucleotide Excision Repair (GG-NER), organism-specific biosystem (from REACTOME)
    Global Genome Nucleotide Excision Repair (GG-NER), organism-specific biosystemThe DNA damage in GG-NER is recognized by the joint action of two protein complexes. The first complex is composed of XPC, RAD23A or RAD23B and CETN2. The second complex, known as the UV-DDB complex,...
  • HDR through MMEJ (alt-NHEJ), organism-specific biosystem (from REACTOME)
    HDR through MMEJ (alt-NHEJ), organism-specific biosystemHomology directed repair (HDR) through microhomology-mediated end joining (MMEJ) is an error prone process also known as alternative nonhomologous end joining (alt-NHEJ), although it does not involve...
  • Homology Directed Repair, organism-specific biosystem (from REACTOME)
    Homology Directed Repair, organism-specific biosystemHomology directed repair (HDR) of DNA double strand breaks (DSBs) requires resection of DNA DSB ends. Resection creates 3'-ssDNA overhangs which then anneal with a homologous DNA sequence. This homol...
  • Nucleotide Excision Repair, organism-specific biosystem (from REACTOME)
    Nucleotide Excision Repair, organism-specific biosystemNucleotide excision repair (NER) was first described in the model organism E. coli in the early 1960s as a process whereby bulky base damage is enzymatically removed from DNA, facilitating the recove...
  • Resolution of AP sites via the single-nucleotide replacement pathway, organism-specific biosystem (from REACTOME)
    Resolution of AP sites via the single-nucleotide replacement pathway, organism-specific biosystemThe single nucleotide replacement pathway of base excision repair appears to facilitate the repair of most damaged bases. Following DNA glycosylase mediated cleavage of the damaged base, the endonucl...
  • Resolution of Abasic Sites (AP sites), organism-specific biosystem (from REACTOME)
    Resolution of Abasic Sites (AP sites), organism-specific biosystemResolution of AP sites can occur through the single nucleotide replacement pathway or through the multiple nucleotide patch replacement pathway, also known as the long-patch base excision repair (BER...
  • Transcription-Coupled Nucleotide Excision Repair (TC-NER), organism-specific biosystem (from REACTOME)
    Transcription-Coupled Nucleotide Excision Repair (TC-NER), organism-specific biosystemDNA damage in transcribed strands of active genes is repaired through a specialized nucleotide excision repair (NER) pathway known as transcription-coupled nucleotide excision repair (TC-NER). TC-NER...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA ligase (ATP) activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA ligase activity IDA
Inferred from Direct Assay
more info
PubMed 
DNA ligase activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
DNA biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
NOT V(D)J recombination IDA
Inferred from Direct Assay
more info
PubMed 
base-excision repair, DNA ligation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
base-excision repair, DNA ligation IDA
Inferred from Direct Assay
more info
PubMed 
base-excision repair, DNA ligation TAS
Traceable Author Statement
more info
 
cell cycle IEA
Inferred from Electronic Annotation
more info
 
cell division IEA
Inferred from Electronic Annotation
more info
 
double-strand break repair IDA
Inferred from Direct Assay
more info
PubMed 
double-strand break repair via alternative nonhomologous end joining IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
double-strand break repair via homologous recombination TAS
Traceable Author Statement
more info
 
lagging strand elongation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrial DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
negative regulation of mitochondrial DNA replication IMP
Inferred from Mutant Phenotype
more info
PubMed 
nucleotide-excision repair, DNA gap filling TAS
Traceable Author Statement
more info
 
transcription-coupled nucleotide-excision repair TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
DNA ligase 3
Names
ligase II, DNA, ATP-dependent
ligase III, DNA, ATP-dependent
polydeoxyribonucleotide synthase [ATP] 3
NP_002302.2
NP_039269.2
XP_005258027.1
XP_006721959.1
XP_016880113.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029221.1 RefSeqGene

    Range
    5001..29572
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_002311.4NP_002302.2  DNA ligase 3 isoform beta precursor

    See identical proteins and their annotated locations for NP_002302.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (beta) contains an alternate in-frame exon in the coding region which includes an in-frame stop codon, compared to variant alpha. This isoform (beta) is shorter and has a distinct C-terminus, compared to isoform alpha.
    Source sequence(s)
    BG470103, DB100562, U40671
    Consensus CDS
    CCDS11285.2
    UniProtKB/Swiss-Prot
    P49916
    Related
    ENSP00000262327.4, OTTHUMP00000163854, ENST00000262327.9, OTTHUMT00000256455
    Conserved Domains (5) summary
    cd07967
    Location:686824
    OBF_DNA_ligase_III; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit
    cd07902
    Location:468680
    Adenylation_DNA_ligase_III; Adenylation domain of DNA Ligase III
    TIGR00574
    Location:318830
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97179
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam04675
    Location:264429
    DNA_ligase_A_N; DNA ligase N terminus
  2. NM_013975.3NP_039269.2  DNA ligase 3 isoform alpha precursor

    See identical proteins and their annotated locations for NP_039269.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (alpha) represents the longer transcript and encodes the longer isoform (alpha).
    Source sequence(s)
    AA872458, AW166526, BC068005, BM726768, DB100562
    Consensus CDS
    CCDS11284.2
    UniProtKB/Swiss-Prot
    P49916
    Related
    ENSP00000367787.3, OTTHUMP00000158641, ENST00000378526.8, OTTHUMT00000250330
    Conserved Domains (3) summary
    TIGR00574
    Location:318830
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:96181
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:9331004
    LIG3_BRCT; DNA ligase 3 BRCT domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p12 Primary Assembly

    Range
    34980498..35005828
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005257970.4XP_005258027.1  DNA ligase 3 isoform X1

    Conserved Domains (6) summary
    cd07967
    Location:695833
    OBF_DNA_ligase_III; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit
    cd07902
    Location:477689
    Adenylation_DNA_ligase_III; Adenylation domain of DNA Ligase III
    TIGR00574
    Location:327839
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:106188
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam04675
    Location:273438
    DNA_ligase_A_N; DNA ligase N terminus
    pfam16759
    Location:9421013
    LIG3_BRCT; DNA ligase 3 BRCT domain
  2. XM_006721896.3XP_006721959.1  DNA ligase 3 isoform X3

    Conserved Domains (5) summary
    cd07967
    Location:695833
    OBF_DNA_ligase_III; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit
    cd07902
    Location:477689
    Adenylation_DNA_ligase_III; Adenylation domain of DNA Ligase III
    TIGR00574
    Location:327839
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:106188
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam04675
    Location:273438
    DNA_ligase_A_N; DNA ligase N terminus
  3. XM_017024624.1XP_016880113.1  DNA ligase 3 isoform X2

    UniProtKB/Swiss-Prot
    P49916
    Conserved Domains (3) summary
    TIGR00574
    Location:318830
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:96181
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:9331004
    LIG3_BRCT; DNA ligase 3 BRCT domain
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